The Puritans had struggled and sacrificed to protect their independence and their state religion. The Quakers attacked both. They loudly 'trespassed' in Boston and other towns. Quakers burst into church services, disrupted baptisms, shouted in the streets, sent letters to ministers questioning their religion and predicted great calamities that would fall on New England.
The Puritans responded harshly to the Quaker troublemakers, imposing severe punishments. They cut off Quaker ears, bored through Quaker tongues and hanged Quakers. From 1659 to 1661, four Quakers, including Mary Dyer, were hanged as Quakers in Boston.
The Puritans didn't want to invite a crackdown by the English government. Slowly and grudgingly they began to tolerate Quakers. And Quakers eventually stopped confronting Puritans, becoming mainstream New Englanders.
It was a very slow process, though. Samuel Sewall, for example, described a Quaker disturbance during a sermon on July 8, 1677: "there came in a female Quaker, in a Canvas Frock, her hair disheveled and loose like a Periwigg, her face as black as ink, led by two other Quakers, and two others followed. It occasioned the greatest and most amazing uproar that I ever saw."
It wasn't until 1685 that the Massachusetts General Court annulled a law sentencing Quakers to death for returning from banishment.
On June 21, 1677, Samuel Sewall wrote in his diary:
June 21, 1677. Just at the end of the Sermon (it made Mr. Allen break off the more abruptly) one Torrey, of Roxbury, gave a suddain and amazing cry which disturbed the whole Assembly. It seems he had the falling sickness. Tis to be feared the Quaker disturbance and this are ominous.